RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:06:01 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/2_msa/P51956_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/3_mltree/P51956.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646361 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/2_msa/P51956_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 506 sites WARNING: Sequences tr_G1R4E6_G1R4E6_NOMLE_61853 and tr_H2QQE9_H2QQE9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8L8I7_A0A2J8L8I7_PANTR_9598 and sp_P51956_NEK3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QND7_H2QND7_PANTR_9598 and tr_A0A2R8ZM43_A0A2R8ZM43_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0G950_A0A0E0G950_ORYNI_4536 and tr_B8AEP6_B8AEP6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0G950_A0A0E0G950_ORYNI_4536 and tr_A0A0E0NH44_A0A0E0NH44_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G950_A0A0E0G950_ORYNI_4536 and sp_Q6YY75_NEK6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HF49_A0A0E0HF49_ORYNI_4536 and tr_B8AYQ1_B8AYQ1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HF49_A0A0E0HF49_ORYNI_4536 and tr_I1PW22_I1PW22_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HF49_A0A0E0HF49_ORYNI_4536 and tr_A0A0D3G870_A0A0D3G870_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HF49_A0A0E0HF49_ORYNI_4536 and tr_A0A0D9ZZT7_A0A0D9ZZT7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HXB1_A0A0E0HXB1_ORYNI_4536 and tr_B8B7P0_B8B7P0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HXB1_A0A0E0HXB1_ORYNI_4536 and tr_I1Q8H6_I1Q8H6_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HXB1_A0A0E0HXB1_ORYNI_4536 and tr_A0A0E0Q4R1_A0A0E0Q4R1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HXB1_A0A0E0HXB1_ORYNI_4536 and sp_Q6ZEZ5_NEK3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and sp_A2ZMH2_NEK2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and tr_I1R7P0_I1R7P0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and tr_A0A0E0FDY0_A0A0E0FDY0_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and tr_A0A0E0RJQ5_A0A0E0RJQ5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and tr_A0A0D3HWJ0_A0A0D3HWJ0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and tr_A0A0E0BUY7_A0A0E0BUY7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0JC51_A0A0E0JC51_ORYNI_4536 and sp_Q2QMH1_NEK2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7GZ09_F7GZ09_MACMU_9544 and tr_A0A2K6DRZ8_A0A2K6DRZ8_MACNE_9545 are exactly identical! WARNING: Sequences tr_I1NTM5_I1NTM5_ORYGL_4538 and tr_A0A0E0N5G2_A0A0E0N5G2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1NTM5_I1NTM5_ORYGL_4538 and tr_A0A0D3EWN0_A0A0D3EWN0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1NTM5_I1NTM5_ORYGL_4538 and sp_Q94CU5_NEK5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1P1Q3_I1P1Q3_ORYGL_4538 and tr_A0A0D3F711_A0A0D3F711_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PDR5_I1PDR5_ORYGL_4538 and tr_A0A0E0NYL6_A0A0E0NYL6_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1PDR5_I1PDR5_ORYGL_4538 and tr_A0A0D3FLK1_A0A0D3FLK1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PDR5_I1PDR5_ORYGL_4538 and sp_Q10GB1_NEK1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B3RKK0_B3RKK0_TRIAD_10228 and tr_A0A369SCZ5_A0A369SCZ5_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4ER12_M4ER12_BRARP_51351 and tr_A0A0D3CHW0_A0A0D3CHW0_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A3B6LEX4_A0A3B6LEX4_WHEAT_4565 and tr_A0A3B6ML24_A0A3B6ML24_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067ETM5_A0A067ETM5_CITSI_2711 and tr_V4U650_V4U650_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FBN0_A0A067FBN0_CITSI_2711 and tr_A0A2H5P4A4_A0A2H5P4A4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067FMM6_A0A067FMM6_CITSI_2711 and tr_V4U507_V4U507_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A1S3Z119_A0A1S3Z119_TOBAC_4097 and tr_A0A1U7VXL2_A0A1U7VXL2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4ABK5_A0A1S4ABK5_TOBAC_4097 and tr_A0A1U7W9V6_A0A1U7W9V6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C2K8_A0A1S4C2K8_TOBAC_4097 and tr_A0A1U7VSE2_A0A1U7VSE2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DIJ5_A0A1S4DIJ5_TOBAC_4097 and tr_A0A1U7XGW0_A0A1U7XGW0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3JQB1_A0A1S3JQB1_LINUN_7574 and tr_A0A1S3JR21_A0A1S3JR21_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3VF22_A0A1S3VF22_VIGRR_3916 and tr_A0A3Q0FJR5_A0A3Q0FJR5_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1U8G1X8_A0A1U8G1X8_CAPAN_4072 and tr_A0A2G3CUN2_A0A2G3CUN2_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.reduced.phy Alignment comprises 1 partitions and 506 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 506 Gaps: 22.99 % Invariant sites: 0.40 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/3_mltree/P51956.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 127 / 10160 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -246088.067698 [00:00:00 -246088.067698] Initial branch length optimization [00:00:01 -236164.996465] Model parameter optimization (eps = 0.100000) [00:00:52] Tree #1, final logLikelihood: -235406.609074 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.119249,0.181674) (0.174955,0.197684) (0.220841,0.683464) (0.484955,1.634818) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51956/4_raxmlng_ancestral/P51956.raxml.log Analysis started: 02-Jun-2021 18:06:01 / finished: 02-Jun-2021 18:06:58 Elapsed time: 57.269 seconds Consumed energy: 3.432 Wh